Bioinformatician II - Division of Viral Diseases

Ihrcorporated•Atlanta, GA

3d•Remote

About The Position

IHRC Inc. seeks a Bioinformatician II to provide technical support to the Centers for Disease Control and Prevention (CDC), Division of Viral Diseases (DVD), Viral Vaccine and Preventable Diseases Branch (VVPDB). The role supports viral genomic surveillance, sequence analysis, laboratory bioinformatics operations, and genomic epidemiology. It performs routine and moderately complex analyses and maintains computational workflows under the general direction of senior scientific or bioinformatics staff. The position is remote, with the ability to travel to a CDC location in Atlanta when needed. Travel expenses are not provided. Work includes processing and analyzing next-generation sequencing data; developing, testing, validating, and maintaining reproducible pipelines; supporting laboratory and surveillance data systems; conducting phylogenetic and genomic epidemiologic analyses; and preparing technical and scientific products. The role also supports quality control, troubleshooting, documentation, database activities, and collaboration with laboratory scientists, epidemiologists, bioinformaticians, and other project personnel.

Requirements

Experience performing bioinformatics analysis in a research, clinical, public health, or comparable scientific environment.
Experience independently executing established analytical workflows and performing moderately complex bioinformatics assignments with general technical direction.
Experience processing and performing quality control on next-generation sequencing data.
Experience with amplicon-based and/or hybrid-capture sequencing methods.
Experience with viral genome assembly, reference-based analysis, consensus generation, and variant analysis.
Experience with Linux command-line environments.
Experience with Python, R, and Bash scripting.
Experience with Git or comparable version-control systems.
Experience developing reproducible workflows using Nextflow or a comparable workflow-management system.
Experience with Docker and/or Apptainer/Singularity containerization.
Experience with HPC or cluster computing environments.
Experience with phylogenetic analysis and associated software.
Experience with genomic epidemiology or pathogen genomic surveillance.
Experience managing and analyzing sequencing metadata.
Experience with LIMS or comparable laboratory/data-management systems.
Experience with SQL and relational database concepts.
Education and experience: MS with 1–3 years of experience, or PhD/postdoctoral experience with at least 1 year of experience.

Nice To Haves

Experience with Hadoop or comparable distributed data-processing technologies, when applicable to the assignment.
Experience developing or optimizing genomic databases, when applicable to the assignment.
Experience with tools such as minimap2, BWA-MEM/BWA-MEM2, Bowtie2, SAMtools, FastQC, MultiQC, iVar, and IGV.
Experience with phylogenetic or phylodynamic tools such as IQ-TREE, RAxML/RAxML-NG, BEAST, and Nextstrain.

Responsibilities

Perform routine and moderately complex bioinformatics analyses and support viral genomic surveillance, sequence analysis, laboratory bioinformatics operations, and genomic epidemiology.
Develop, revise, document, implement, and maintain SOPs, technical procedures, quality documentation, job aids, and supporting pipeline and laboratory workflow documentation.
Perform production-level quality control, processing, and analysis of NGS data generated internally or received from external laboratories.
Process and evaluate genomic data formats, including FASTQ, BAM/CRAM, VCF, and FASTA, along with sequencing and sample metadata.
Use bioinformatics software for sequence alignment, read processing, quality assessment, variant analysis, genome assembly, and visualization.
Identify, investigate, document, and help resolve data-quality, metadata, pipeline, analysis, and data-exchange issues.
Support genomic data processing from receipt of sequencing data and metadata through quality assessment, analysis, review, reporting, archiving, and submission to relevant databases or surveillance systems.
Develop, configure, test, validate, implement, and maintain reproducible viral sequence-analysis pipelines and workflows using established tools, approved methods, version-controlled code, and documented computational environments.
Use Linux-based computational methods and scripting to automate, optimize, and troubleshoot workflows; run containerized workflows in HPC or cluster environments.
Support integration of bioinformatics workflows and genomic data products with laboratory, computational, surveillance, and data-management platforms.
Access and support data-management activities in LIMS and other systems used to track specimens, sequencing data, analytical results, and metadata.
Analyze viral amplicon-based and hybrid-capture NGS data, including read processing, reference-based analysis, assembly, consensus generation, variant identification, and quality assessment.
Conduct phylogenetic and genomic epidemiologic analyses, including analyses of viral evolution, transmission patterns, genetic diversity, lineage or clade distributions, and emerging genomic trends.
Support genomic epidemiologic studies of viral evolution and emerging variants, including analyses of mutations and geographic and temporal trends relevant to public health surveillance and response.
Evaluate results against established quality criteria and follow approved protocols and documented procedures for analyses, workflows, and quality control.
Troubleshoot computational issues, data-format inconsistencies, sequence-quality problems, and workflow errors; document corrective actions or recommended solutions.
Develop, query, maintain, and validate genomic or sequence-related databases and structured datasets; support relational database development and optimization when assigned.
Provide genomic subject-matter support for assigned viral pathogens or virus families, including input on methods, quality, lineage or clade interpretation, surveillance findings, and genomic data products.
Prepare reports, summaries, dashboards, tables, figures, presentations, and other products communicating findings, metrics, results, workflow performance, or project accomplishments.
Contribute analyses, figures, methods, technical content, and documentation to abstracts, posters, presentations, technical reports, manuscripts, publications, and other scientific or surveillance products.
Collaborate with laboratory scientists, epidemiologists, bioinformaticians, data scientists, informaticians, and other project personnel to meet genomic surveillance requirements and complete assigned activities.